DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes

Reis, L. Aparecida; Rocha, M. S.

doi:10.1002/bip.23015

Cited by 22 publications

(9 citation statements)

References 44 publications

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“…The radius of curvature of DAPI-incubated 6HB-Arc gradually reduced up to 32% in 8 μM concentration without noticeable out-of-plane deformation, resulting in the formation of closed circles as shown in AFM images (Figure 3B and D – E , and Supplementary Figure S48 ). Similar to the decrement in the bending persistence length of DAPI-incubated straight 6HB structures, we attribute this behavior to the additional intercalating mode of DAPI that appears in higher molecular concentrations as well ( 57 ). Increased portion of the non-circular structures observed in 32 μM concentration supports this hypothesis that an increased amount of intercalation might have a negative impact on the structure to maintain its planar geometry ( Supplementary Figure S48 ).…”

Section: Resultssupporting

confidence: 53%

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Lee

Kim

et al. 2021

Nucleic Acids Research

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Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.

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Section: Resultssupporting

confidence: 53%

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Lee

Kim

et al. 2021

Nucleic Acids Research

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“…Such binding is expected to stiffen the DNA but should not result in major changes of the double helix structure. However, at higher concentrations, intercalation also occurs [25] and under such conditions H1.1 was detached from DNA (Figure 5(I,J)). These observations confirm that DNA helix distortion causes detachment of histone H1, and are in agreement with previously reported higher mobility of the linker histone H1.1 induced by exposure to daunomycin [14].…”

Section: Resultsmentioning

confidence: 99%

Translocation of chromatin proteins to nucleoli—The influence of protein dynamics on post‐fixation localization

et al. 2021

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It is expected that the subnuclear localization of a protein in a fixed cell, detected by microscopy, reflects its position in the living cell. We demonstrate, however, that some dynamic nuclear proteins can change their localization upon fixation by either crosslinking or non-crosslinking methods. We examined the subnuclear localization of the chromatin architectural protein HMGB1, linker histone H1, and core histone H2B in cells fixed by formaldehyde, glutaraldehyde, glyoxal, ethanol, or zinc salts. We demonstrate that some dynamic, weakly binding nuclear proteins, like HMGB1 and H1, may not only be unexpectedly lost from their original binding sites during the fixation process, but they can also diffuse through the nucleus and eventually bind in nucleoli. Such translocation to nucleoli does not occur in the case of core histone H2B, which is more stably bound to DNA and other histones. We suggest that the diminished binding of some dynamic proteins to DNA during fixation, and their subsequent translocation to nucleoli, is induced by changes of DNA structure, arising from interaction with a fixative. Detachment of dynamic proteins from chromatin can also be induced in cells already fixed by non-crosslinking methods when DNA structure is distorted by intercalating molecules. The proteins translocated during fixation from chromatin to nucleoli bind there to RNA-containing structures.

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“…In particular, this methodology provides structural parameters of the intercalated mole-cule such as the DNA length increase (12), the degree of untwisting (13)(14)(15), and the binding site size (12,14). Furthermore, affinity constants (12,15), different binding modes (11,(16)(17)(18), and the kinetics of association and dissociation (19)(20)(21)(22) can be evaluated.…”

Section: Introductionmentioning

confidence: 99%

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

Dikic

Seidel

2019

Biophysical Journal

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DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the forceextension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.

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DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes

Cited by 22 publications

References 44 publications

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Translocation of chromatin proteins to nucleoli—The influence of protein dynamics on post‐fixation localization

Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA

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